data_DUX
#
_chem_comp.id DUX
_chem_comp.name "2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C28 H25 F N2 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-05-05
_chem_comp.pdbx_modified_date 2021-03-13
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 472.508
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DUX
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1VYQ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
# #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
DUX "F3'" "F3'" F 0 1 N N N 37.829 -8.962 -12.615 4.088 -0.520 -1.486 "F3'" DUX 1
DUX "C3'" "C3'" C 0 1 N N S 37.380 -9.638 -11.556 2.848 0.127 -1.494 "C3'" DUX 2
DUX "C2'" "C2'" C 0 1 N N N 36.218 -10.547 -11.964 2.346 0.319 -2.945 "C2'" DUX 3
DUX "C1'" "C1'" C 0 1 N N R 36.522 -11.802 -11.163 1.376 -0.877 -3.114 "C1'" DUX 4
DUX N1 N1 N 0 1 N N N 35.940 -11.840 -9.817 0.380 -0.592 -4.150 N1 DUX 5
DUX C2 C2 C 0 1 N N N 35.849 -13.104 -9.174 -0.448 0.457 -4.006 C2 DUX 6
DUX N3 N3 N 0 1 N N N 35.303 -13.186 -7.936 -1.369 0.744 -4.944 N3 DUX 7
DUX C4 C4 C 0 1 N N N 34.865 -12.083 -7.278 -1.482 -0.026 -6.045 C4 DUX 8
DUX C5 C5 C 0 1 N N N 34.951 -10.821 -7.863 -0.620 -1.137 -6.206 C5 DUX 9
DUX C6 C6 C 0 1 N N N 35.494 -10.732 -9.149 0.298 -1.400 -5.252 C6 DUX 10
DUX O4 O4 O 0 1 N N N 34.402 -12.157 -6.131 -2.319 0.230 -6.892 O4 DUX 11
DUX O2 O2 O 0 1 N N N 36.272 -14.117 -9.780 -0.358 1.161 -3.019 O2 DUX 12
DUX "O4'" "O4'" O 0 1 N N N 37.944 -11.828 -10.984 0.749 -0.988 -1.818 "O4'" DUX 13
DUX "C4'" "C4'" C 0 1 N N R 38.522 -10.505 -11.094 1.774 -0.757 -0.832 "C4'" DUX 14
DUX "C5'" "C5'" C 0 1 N N N 39.152 -9.953 -9.822 1.176 -0.042 0.380 "C5'" DUX 15
DUX "O5'" "O5'" O 0 1 N N N 40.521 -10.439 -9.666 0.170 -0.868 0.971 "O5'" DUX 16
DUX C17 C17 C 0 1 N N N 41.140 -10.542 -8.348 -0.272 -0.197 2.153 C17 DUX 17
DUX C30 C30 C 0 1 Y N N 41.722 -9.167 -8.013 0.853 -0.144 3.153 C30 DUX 18
DUX C31 C31 C 0 1 Y N N 41.558 -8.049 -8.870 1.894 -1.049 3.070 C31 DUX 19
DUX C32 C32 C 0 1 Y N N 42.112 -6.810 -8.539 2.927 -1.000 3.987 C32 DUX 20
DUX C33 C33 C 0 1 Y N N 42.872 -6.658 -7.374 2.919 -0.045 4.987 C33 DUX 21
DUX C34 C34 C 0 1 Y N N 43.066 -7.753 -6.536 1.878 0.859 5.069 C34 DUX 22
DUX C35 C35 C 0 1 Y N N 42.493 -8.999 -6.843 0.847 0.813 4.149 C35 DUX 23
DUX C24 C24 C 0 1 Y N N 40.038 -11.031 -7.431 -0.701 1.204 1.803 C24 DUX 24
DUX C25 C25 C 0 1 Y N N 39.548 -10.275 -6.365 -2.028 1.472 1.526 C25 DUX 25
DUX C26 C26 C 0 1 Y N N 38.509 -10.752 -5.564 -2.421 2.758 1.205 C26 DUX 26
DUX C27 C27 C 0 1 Y N N 37.909 -11.971 -5.842 -1.487 3.776 1.163 C27 DUX 27
DUX C28 C28 C 0 1 Y N N 38.369 -12.744 -6.904 -0.160 3.508 1.442 C28 DUX 28
DUX C29 C29 C 0 1 Y N N 39.422 -12.275 -7.704 0.231 2.223 1.766 C29 DUX 29
DUX C18 C18 C 0 1 Y N N 42.287 -11.539 -8.474 -1.437 -0.945 2.748 C18 DUX 30
DUX C19 C19 C 0 1 Y N N 43.101 -11.563 -9.624 -2.131 -1.865 1.984 C19 DUX 31
DUX C20 C20 C 0 1 Y N N 44.174 -12.479 -9.729 -3.199 -2.552 2.530 C20 DUX 32
DUX C21 C21 C 0 1 Y N N 44.440 -13.407 -8.711 -3.575 -2.318 3.840 C21 DUX 33
DUX C22 C22 C 0 1 Y N N 43.647 -13.385 -7.564 -2.881 -1.398 4.604 C22 DUX 34
DUX C23 C23 C 0 1 Y N N 42.593 -12.466 -7.456 -1.809 -0.715 4.059 C23 DUX 35
DUX "H3'" "H3'" H 0 1 N N N 37.066 -8.938 -10.747 2.918 1.088 -0.984 "H3'" DUX 36
DUX "H2'1" "1H2'" H 0 0 N N N 36.096 -10.700 -13.062 1.817 1.266 -3.052 "H2'1" DUX 37
DUX "H2'2" "2H2'" H 0 0 N N N 35.201 -10.118 -11.809 3.171 0.254 -3.654 "H2'2" DUX 38
DUX "H1'" "H1'" H 0 1 N N N 36.199 -12.701 -11.737 1.927 -1.787 -3.353 "H1'" DUX 39
DUX H3 H3 H 0 1 N N N 35.219 -14.099 -7.488 -1.957 1.507 -4.827 H3 DUX 40
DUX H5 H5 H 0 1 N N N 34.602 -9.921 -7.329 -0.695 -1.766 -7.081 H5 DUX 41
DUX H6 H6 H 0 1 N N N 35.564 -9.745 -9.636 0.965 -2.243 -5.357 H6 DUX 42
DUX "H4'" "H4'" H 0 1 N N N 39.298 -10.524 -11.894 2.213 -1.706 -0.525 "H4'" DUX 43
DUX "H5'1" "1H5'" H 0 0 N N N 38.530 -10.177 -8.924 1.961 0.152 1.111 "H5'1" DUX 44
DUX "H5'2" "2H5'" H 0 0 N N N 39.104 -8.840 -9.788 0.731 0.900 0.064 "H5'2" DUX 45
DUX H31 H31 H 0 1 N N N 40.987 -8.159 -9.807 1.901 -1.795 2.289 H31 DUX 46
DUX H32 H32 H 0 1 N N N 41.949 -5.944 -9.202 3.741 -1.708 3.923 H32 DUX 47
DUX H33 H33 H 0 1 N N N 43.314 -5.679 -7.122 3.726 -0.008 5.704 H33 DUX 48
DUX H34 H34 H 0 1 N N N 43.675 -7.641 -5.623 1.871 1.605 5.851 H34 DUX 49
DUX H35 H35 H 0 1 N N N 42.647 -9.854 -6.163 0.034 1.521 4.214 H35 DUX 50
DUX H25 H25 H 0 1 N N N 39.988 -9.286 -6.152 -2.758 0.676 1.559 H25 DUX 51
DUX H26 H26 H 0 1 N N N 38.163 -10.155 -4.704 -3.458 2.967 0.988 H26 DUX 52
DUX H27 H27 H 0 1 N N N 37.069 -12.327 -5.223 -1.794 4.780 0.912 H27 DUX 53
DUX H28 H28 H 0 1 N N N 37.907 -13.723 -7.116 0.569 4.303 1.408 H28 DUX 54
DUX H29 H29 H 0 1 N N N 39.773 -12.883 -8.555 1.268 2.014 1.984 H29 DUX 55
DUX H19 H19 H 0 1 N N N 42.900 -10.861 -10.450 -1.838 -2.048 0.961 H19 DUX 56
DUX H20 H20 H 0 1 N N N 44.813 -12.463 -10.628 -3.742 -3.270 1.933 H20 DUX 57
DUX H21 H21 H 0 1 N N N 45.259 -14.139 -8.816 -4.410 -2.853 4.266 H21 DUX 58
DUX H22 H22 H 0 1 N N N 43.849 -14.091 -6.741 -3.174 -1.215 5.627 H22 DUX 59
DUX H23 H23 H 0 1 N N N 41.980 -12.468 -6.539 -1.267 0.002 4.656 H23 DUX 60
# #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
DUX "F3'" "C3'" SING N N 1
DUX "C3'" "C2'" SING N N 2
DUX "C3'" "C4'" SING N N 3
DUX "C3'" "H3'" SING N N 4
DUX "C2'" "C1'" SING N N 5
DUX "C2'" "H2'1" SING N N 6
DUX "C2'" "H2'2" SING N N 7
DUX "C1'" N1 SING N N 8
DUX "C1'" "O4'" SING N N 9
DUX "C1'" "H1'" SING N N 10
DUX N1 C2 SING N N 11
DUX N1 C6 SING N N 12
DUX C2 N3 SING N N 13
DUX C2 O2 DOUB N N 14
DUX N3 C4 SING N N 15
DUX N3 H3 SING N N 16
DUX C4 C5 SING N N 17
DUX C4 O4 DOUB N N 18
DUX C5 C6 DOUB N N 19
DUX C5 H5 SING N N 20
DUX C6 H6 SING N N 21
DUX "O4'" "C4'" SING N N 22
DUX "C4'" "C5'" SING N N 23
DUX "C4'" "H4'" SING N N 24
DUX "C5'" "O5'" SING N N 25
DUX "C5'" "H5'1" SING N N 26
DUX "C5'" "H5'2" SING N N 27
DUX "O5'" C17 SING N N 28
DUX C17 C30 SING N N 29
DUX C17 C24 SING N N 30
DUX C17 C18 SING N N 31
DUX C30 C31 DOUB Y N 32
DUX C30 C35 SING Y N 33
DUX C31 C32 SING Y N 34
DUX C31 H31 SING N N 35
DUX C32 C33 DOUB Y N 36
DUX C32 H32 SING N N 37
DUX C33 C34 SING Y N 38
DUX C33 H33 SING N N 39
DUX C34 C35 DOUB Y N 40
DUX C34 H34 SING N N 41
DUX C35 H35 SING N N 42
DUX C24 C25 DOUB Y N 43
DUX C24 C29 SING Y N 44
DUX C25 C26 SING Y N 45
DUX C25 H25 SING N N 46
DUX C26 C27 DOUB Y N 47
DUX C26 H26 SING N N 48
DUX C27 C28 SING Y N 49
DUX C27 H27 SING N N 50
DUX C28 C29 DOUB Y N 51
DUX C28 H28 SING N N 52
DUX C29 H29 SING N N 53
DUX C18 C19 DOUB Y N 54
DUX C18 C23 SING Y N 55
DUX C19 C20 SING Y N 56
DUX C19 H19 SING N N 57
DUX C20 C21 DOUB Y N 58
DUX C20 H20 SING N N 59
DUX C21 C22 SING Y N 60
DUX C21 H21 SING N N 61
DUX C22 C23 DOUB Y N 62
DUX C22 H22 SING N N 63
DUX C23 H23 SING N N 64
# #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
DUX SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(F)C2)COC(c3ccccc3)(c4ccccc4)c5ccccc5"
DUX SMILES_CANONICAL CACTVS 3.341 "F[C@H]1C[C@@H](O[C@@H]1COC(c2ccccc2)(c3ccccc3)c4ccccc4)N5C=CC(=O)NC5=O"
DUX SMILES CACTVS 3.341 "F[CH]1C[CH](O[CH]1COC(c2ccccc2)(c3ccccc3)c4ccccc4)N5C=CC(=O)NC5=O"
DUX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(c2ccccc2)(c3ccccc3)OC[C@@H]4[C@H](C[C@@H](O4)N5C=CC(=O)NC5=O)F"
DUX SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(c2ccccc2)(c3ccccc3)OCC4C(CC(O4)N5C=CC(=O)NC5=O)F"
DUX InChI InChI 1.03 "InChI=1S/C28H25FN2O4/c29-23-18-26(31-17-16-25(32)30-27(31)33)35-24(23)19-34-28(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22/h1-17,23-24,26H,18-19H2,(H,30,32,33)/t23-,24+,26+/m0/s1"
DUX InChIKey InChI 1.03 GJNIPWYJQUGERM-BFLUCZKCSA-N
# #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
DUX "SYSTEMATIC NAME" ACDLabs 10.04 "2',3'-dideoxy-3'-fluoro-5'-O-trityluridine"
DUX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-4-fluoro-5-(trityloxymethyl)oxolan-2-yl]pyrimidine-2,4-dione"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DUX "Create component" 2004-05-05 EBI
DUX "Modify descriptor" 2011-06-04 RCSB
DUX "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DUX
_pdbx_chem_comp_synonyms.name "1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##